Mercurial > repos > iuc > variant_analyzer

annotate mut2read.py @ 0:5441e79a30f2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
author iuc
date Wed, 20 Nov 2019 22:47:11 +0000
parents
children 833d9e71b864
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5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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1 #!/usr/bin/env python
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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3 """mut2read.py
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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5 Author -- Gundula Povysil
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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6 Contact -- povysil@bioinf.jku.at
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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7
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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8 Takes a tabular file with mutations and a BAM file as input and prints
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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9 all tags of reads that carry the mutation to a user specified output file.
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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10 Creates fastq file of reads of tags with mutation.
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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12 ======= ========== ================= ================================
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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13 Version Date Author Description
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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14 0.2.1 2019-10-27 Gundula Povysil -
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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15 ======= ========== ================= ================================
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17 USAGE: python mut2read.py DCS_Mutations.tabular DCS.bam Aligned_Families.tabular Interesting_Reads.fastq
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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18 tag_count_dict.json
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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19 """
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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21 import argparse
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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22 import json
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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23 import os
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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24 import sys
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26 import numpy as np
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27 import pysam
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30 def make_argparser():
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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31 parser = argparse.ArgumentParser(description='Takes a tabular file with mutations and a BAM file as input and prints all tags of reads that carry the mutation to a user specified output file and creates a fastq file of reads of tags with mutation.')
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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32 parser.add_argument('--mutFile',
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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33 help='TABULAR file with DCS mutations.')
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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34 parser.add_argument('--bamFile',
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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35 help='BAM file with aligned DCS reads.')
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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36 parser.add_argument('--familiesFile',
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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37 help='TABULAR file with aligned families.')
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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38 parser.add_argument('--outputFastq',
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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39 help='Output FASTQ file of reads with mutations.')
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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40 parser.add_argument('--outputJson',
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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41 help='Output JSON file to store collected data.')
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42 return parser
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45 def mut2read(argv):
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46 parser = make_argparser()
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47 args = parser.parse_args(argv[1:])
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49 file1 = args.mutFile
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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50 file2 = args.bamFile
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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51 file3 = args.familiesFile
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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52 outfile = args.outputFastq
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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53 json_file = args.outputJson
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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55 if os.path.isfile(file1) is False:
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56 sys.exit("Error: Could not find '{}'".format(file1))
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58 if os.path.isfile(file2) is False:
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59 sys.exit("Error: Could not find '{}'".format(file2))
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61 if os.path.isfile(file3) is False:
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62 sys.exit("Error: Could not find '{}'".format(file3))
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64 # read mut file
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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65 with open(file1, 'r') as mut:
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66 mut_array = np.genfromtxt(mut, skip_header=1, delimiter='\t', comments='#', dtype='string')
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68 # read dcs bam file
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69 # pysam.index(file2)
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70 bam = pysam.AlignmentFile(file2, "rb")
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72 # get tags
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73 tag_dict = {}
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74 cvrg_dict = {}
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76 if len(mut_array) == 13:
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77 mut_array = mut_array.reshape((1, len(mut_array)))
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78
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79 for m in range(len(mut_array[:, 0])):
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80 print(str(m + 1) + " of " + str(len(mut_array[:, 0])))
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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81 chrom = mut_array[m, 1]
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82 stop_pos = mut_array[m, 2].astype(int)
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
83 chrom_stop_pos = str(chrom) + "#" + str(stop_pos)
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
84 ref = mut_array[m, 9]
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
85 alt = mut_array[m, 10]
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
86
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
87 dcs_len = []
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
88
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
89 for pileupcolumn in bam.pileup(chrom.tobytes(), stop_pos - 2, stop_pos, max_depth=100000000):
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
90
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
91 if pileupcolumn.reference_pos == stop_pos - 1:
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
92 count_alt = 0
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
93 count_ref = 0
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
94 count_indel = 0
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
95 count_n = 0
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
96 count_other = 0
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
97 count_lowq = 0
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
98 print("unfiltered reads=", pileupcolumn.n, "filtered reads=", len(pileupcolumn.pileups),
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
99 "difference= ", len(pileupcolumn.pileups) - pileupcolumn.n)
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
100 for pileupread in pileupcolumn.pileups:
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
101 if not pileupread.is_del and not pileupread.is_refskip:
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
102 # query position is None if is_del or is_refskip is set.
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
103 nuc = pileupread.alignment.query_sequence[pileupread.query_position]
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
104 dcs_len.append(len(pileupread.alignment.query_sequence))
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
105 if nuc == alt:
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
106 count_alt += 1
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
107 tag = pileupread.alignment.query_name
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
108 if tag in tag_dict:
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
109 tag_dict[tag][chrom_stop_pos] = alt
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
110 else:
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
111 tag_dict[tag] = {}
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
112 tag_dict[tag][chrom_stop_pos] = alt
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
113 elif nuc == ref:
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
114 count_ref += 1
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
115 elif nuc == "N":
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
116 count_n += 1
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
117 elif nuc == "lowQ":
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
118 count_lowq += 1
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
119 else:
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
120 count_other += 1
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
121 else:
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
122 count_indel += 1
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
123 dcs_median = np.median(np.array(dcs_len))
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
124 cvrg_dict[chrom_stop_pos] = (count_ref, count_alt, dcs_median)
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
125
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
126 print("coverage at pos %s = %s, ref = %s, alt = %s, other bases = %s, N = %s, indel = %s, low quality = %s, median length of DCS = %s\n" %
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
127 (pileupcolumn.pos, count_ref + count_alt, count_ref, count_alt, count_other, count_n,
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
128 count_indel, count_lowq, dcs_median))
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
129 bam.close()
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
130
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
131 with open(json_file, "w") as f:
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
132 json.dump((tag_dict, cvrg_dict), f)
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
133
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
134 # create fastq from aligned reads
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
135 with open(outfile, 'w') as out:
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
136 with open(file3, 'r') as families:
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
137 for line in families:
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
138 line = line.rstrip('\n')
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
139 splits = line.split('\t')
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
140 tag = splits[0]
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
141
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
142 if tag in tag_dict:
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
143 str1 = splits[4]
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
144 curr_seq = str1.replace("-", "")
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
145 str2 = splits[5]
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
146 curr_qual = str2.replace(" ", "")
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
147
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
148 out.write("@" + splits[0] + "." + splits[1] + "." + splits[2] + "\n")
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
149 out.write(curr_seq + "\n")
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
150 out.write("+" + "\n")
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
151 out.write(curr_qual + "\n")
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
152
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
153
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
154 if __name__ == '__main__':
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
155 sys.exit(mut2read(sys.argv))